How to model a pitched roof?
First off there is no reason to be adding a cube up there to fill in the roof, you could simply do that (in edit mode) by adding a loop cut (CtrlR then right click or Esc to cancel the movement so the new loop jumps to the center) in the base cube then moving the new edge up to meet the peak of the roof.





If you did want a separate cube for the top and bottom of your house, you still do not need the knife tool. First scale up the cube to match the size of the bottom cube and bottom of the roof. Then simply select the top four vertices of that cube and use the two most basic modeling tools G Grab to move, and S Scale to change the size, to position it to match your roof.
I have an animated gif below.




For the "super thin" roof, you could add a Solidify modifier Planes are two dimensional, so by definition that will be super thin. You need to add geometry (by modeling or modifiers) to create that third dimension.